Ran into the same thing. Don't know enough about how dependencies are specified in ebuild files to say exactly what the problem is, but I worked around it by creating an overlay for virtual/modutils (called it modutils-1 to make sure it overrides the buggy version) with all dependencies removed. I was then able to emerge kmod.

what does that do for you?_________________The best argument against democracy is a five-minute conversation with the average voter
Great Britain is a republic, with a hereditary president, while the United States is a monarchy with an elective king

Besides, I would understand that this would actually cause an error since virtual/modutils requires either kmod with the tools useflag or modutils sysapp or module-init-tools! However, having the tools use flag defined does not make sense to me why this causes trouble!